HMGB1 high affinity binding domain Box-A mutants

ABSTRACT

The present invention relates to polypeptide variants of the HMGB-1 high affinity binding domain Box-A (HMGB1 Box-A) or to a biologically active fragment of HMGB1 Box-A, which are obtained through systematic mutations of single amino acids of the wild-type HMGB1 Box-A protein and which show an increased resistance to proteases and which are therefore characterized by more favorable pharmacokinetic and pharmacodynamic profiles. Moreover, the present invention concerns the use of said polypeptide molecules of HMGB1 Box-A to diagnose, prevent, alleviate and/or treat pathologies associated with extracellular HMGB1 and associated with RAGE.

This application is a divisional of Ser. No. 11/713, 789 filed Mar. 5, 2007, granted as U.S. Pat. No. 7,635,679, which is a continuation in part of PCT/EP2005/009528 filed Sep. 5, 2005; which claims the benefit of European Patent Application No. 04 425 665.9 filed on Sep. 3, 2004, the disclosure of which is incorporated herein in its entirety by reference.

The present invention relates to polypeptide variants of the HMGB-1 high affinity binding domain Box-A (HMGB1 Box-A) or to a biologically active fragment of HMGB1 Box-A, which are obtained through systematic mutations of single amino acids of the wild-type HMGB1 Box-A protein and which show an increased resistance to proteases and which are therefore characterized by more favourable pharmacokinetic and pharmacodynamic profiles. Moreover, the present invention concerns the use of said polypeptide molecules of HMGB1 Box-A to diagnose, prevent, alleviate and/or treat pathologies associated with extracellular HMGB1 and associated with the receptor RAGE.

Recent research in the field of sepsis and inflammation has led to an improved understanding of the pathogenic mechanisms and events underlying their clinical onset and development. In the early stages of sepsis, for instance, bacterial endotoxins stimulate cells of the innate immune system which release pro-inflammatory cytokines (TNF, IL-1α and IL-6). These early cytokines in turn induce the release of a later-acting downstream mediator (identified as the known protein HMGB1) that triggers the pathological sequelae mediated by the subsequent release of cytokines such as TNF, IL-1α, IL-1β, IL-1Ra, IL-6, IL-8, IL-18, IFN-γ, PAF, etc., leading to a multisystem pathogenesis or to a lethal systemic inflammation (Andersson et al., 2002).

The HMGB1 protein belongs to the family of high mobility group (HMG) proteins. HMG proteins, so-called due to their high electrophoretic mobility in polyacrylamide gels, are the most ubiquitous non-histone proteins associated with isolated chromatin in eukaryotic cells. These proteins play a generalized “architectural” role in DNA bending, looping, folding and wrapping, since they either distort, bend or modify DNA structures and complexes with transcription factors or histones (Andersson et al., 2002; Agresti et al., 2003; Degryse et al., 2003). The high mobility group 1 (HMGB1) protein is usually a nuclear factor, in particular a transcriptional regulatory molecule causing DNA bending and facilitating the binding of several transcriptional complexes.

Structurally, the HMGB1 protein is a protein of approximately 25 kDa with a highly conserved sequence among mammals, whereby 2 out of 214 amino acids have conservative substitutions in all mammalian species. HMGB1 is ubiquitously present in all vertebrate nuclei and in particular can be found in fibroblasts, neurons, hepatocytes, glia and in cells derived from hematopoietic stem cells, including monocytes/macrophages, neutrophils and platelets. The HMGB1 molecule has a tripartite structure composed of three distinct domains: two DNA binding domains called HMG Box-A and Box-B, and an acid carboxyl terminus, making it bipolarly charged.

The two HMGB1 boxes are involved in the protein's function as non-sequence-specific architectural DNA-binding elements, conferring the ability to bind DNA into recognized distorted DNA structures and stabilizing nucleosome assembly, remodelling and sliding. Both the A- and B-HMG boxes are made up of highly conserved 84 amino acid residues, are strongly positively charged and are arranged in three α-helices having a similar L-shaped fold. The long arm of the “L” contains the N-terminal extended strand and helix III (Andersson et al. 2002; Agresti et al., 2003; Thomas, J. O. 2001), while the short arm comprises helices I and II. Structure-function analysis reveals that the pro-inflammatory cytokine domain of HMGB1 is the B-Box and in particular the sequence of its first 20 amino acids. The A-Box is an extremely weak agonist of the inflammatory cytokine release triggered by HMGB1 and competitively inhibits the pro-inflammatory activities of the B-Box and of the whole protein. Therefore, from a pharmacological point of view, the A-Box acts as an antagonist of the pathological conditions induced and/or sustained by the B-Box and HMGB1.

The third domain, the carboxyl terminus or acidic tail, is extremely negatively charged since it contains 30 repetitive aspartic and glutamic acid residues, and is linked to the boxes by a basic region of about 20 residues. Mouse and rat HMGB1 differ from the human form by only two substitutions that are located in this continuous C-terminal stretch.

HMGB1 binds rather weakly to the B-form variety of linear double-stranded DNA with no sequence specificity, while it binds in the interior of the nucleus with high affinity to supercoiled DNA, to unusual DNA structures like 4-way junctions (cruciform DNA), bulged DNA and bent DNA (Ferrari et al., 1992; Pontiggia et al., 1993 and PCT/EP2005/007198 in the name of Creabilis Therapeutics).

Besides its nuclear location and role as a transcription factor regulator, HMGB1 has also been found in the extracellular medium, actively released by activated cells of the immune systems (monocytes and macrophages) or passively released by damaged or necrotic cells (Andersson et al., 2002; Scaffidi et al., 2002; Bonaldi et al., 2002; Taniguchi et al., 2003; Friedman et al., 2003; Palumbo et al., 2004).

Extracellularly released HMGB1 acts as a potent cytokine and as an extremely potent macrophage-stimulating factor. HMGB1 acts directly by binding to the cell membrane, inducing signaling and chemotaxis, having a chemokine-like function (Yang et al., 2001) and further acting indirectly by up-regulating the expression and secretion of pro-inflammatory cytokines. This makes extracellular HMGB1 protein a potent chemotactic and immunoregulatory protein which promotes an effective inflammatory immune response. Furthermore, other proteins belonging to the family of HMG proteins, and which are able to bend DNA, are released together with HMGB1 in the extracellular medium. These proteins are inter alia HMGB2, HMGB3, HMG-1L10, HMG-4L and SP100-HMG. They share with HMGB1 highly homologous amino acid sequences. Like HMGB1, they trigger/sustain inflammatory pathologies interacting with the same receptors, leading to the same downstream pathways of interaction.

In healthy cells, HMGB1 migrates to the cytoplasm both by passive and active transport. However, all cultured cells and resting monocytes contain the vast majority of HMGB1 in the nucleus, indicating that in baseline conditions import is much more effective than export. Cells might transport HMGB1 from the nucleus by acetylating lysine residues which are abundant in HMGB1, thereby neutralizing their basic charge and rendering them unable to function as nuclear localization signals. Nuclear HMGB1 hyperacetylation determines the relocation of this protein from the nucleus to the cytoplasm (in the fibroblasts, for example) or its accumulation into secretory endolysosomes (in activated monocytes and macrophages, for example) and subsequent redirection towards release through a non-classical vesicle-mediated secretory pathway. HMGB1 secretion by already activated monocytes is then triggered by bioactive lysophosphatidylcholine (LPC), which is generated later in the inflammation site from phosphatidylcholine through the action of the secretory phospholipase sPLA2 produced by monocytes several hours after activation. Therefore, secretion of HMGB1 seems to be induced by two signals (Bonaldi et al., 2003) and to take place in three steps: 1) at first, an inflammatory signal promotes HMGB1 acetylation and its relocation from the nucleus to the cytoplasm (step 1) and storage in cytoplasmic secretory vesicles (step 2); then, a secretion signal (extracellular ATP or lysophosphatidylcholine) promotes exocytosis (third step) (Andersson et al., 2002; Scaffidi et al. 2002; Gardella et al., 2002; Bonaldi et al., 2003; Friedman et al., 2003).

Released HMGB1 has been identified as one of the ligands binding to the RAGE receptor. This receptor is expressed in most cell types, and at a high level mainly in endothelial cells, in vascular smooth muscle cells, in monocytes and macrophages and in mononuclear phagocytes. Recognition involves the C-terminal of HMGB1. The interaction of HMGB1 and RAGE triggers a sustained period of cellular activation mediated by RAGE up-regulation and receptor-dependent signaling. In particular, the interaction of HMGB1 and RAGE activates several intracellular signal transduction pathways, including mitogen-activated protein kinases (MAPKs), Cdc-42, p21ras, Rac and the nuclear translocation factor KB (NF-κB), the transcription factor classically linked to inflammatory processes (Schmidt et al., 2001).

According to several experimental evidences, released HMGB1 may also interact with receptors belonging to one or more subclasse(s) of the family of the Toll-like receptors. Further, HMGB1 may also interact with the functional N-terminal lectin-like domain (D1) of thrombomodulin. Due to the ability of the functional D1 domain of thrombomodulin to intercept and bind circulating HMGB1, the interaction with the RAGE receptors and the Toll-like receptors is prevented.

In the context of the present invention, “HMGB1” includes the non-acetylated form or/and the acetylated form of HMGB1. Likewise, “HMGB1 homologous proteins” include the non-acetylated form or/and the acetylated form of HMGB1 homologous proteins. Preferred HMGB1 homologous proteins are HMGB2, HMGB3, HMG-1L10, HMG-4L or/and SP100-HMG.

When released in vivo, HMGB1 is an extremely potent cytokine and a potent macrophage-stimulating factor. In fact, like other cytokine mediators of endotoxemia, HMGB1 activates in vitro a cascade of multiple pro-inflammatory cytokines (TNF, IL-1α, IL-1β, IL-1Ra IL-6, IL-8, MIP-1α and MIP-1β) from human macrophages. Therefore, HMGB1 acts as a late mediator during acute inflammation and participates in an important way in the pathogenesis of systemic inflammation after the early mediator response has been resolved.

The observed pro-inflammatory effects of HMGB1 in vitro and the correlation between circulating HMGB1 levels and the development of the pathogenic sequence of systemic inflammation in vivo indicate that therapeutically targeting of this cytokine-like molecule should be of relevant clinical value, suggesting novel therapeutic approaches by a “late” administration of (selective) antagonists/inhibitors of the extracellular activities of HMGB1.

Moreover the observed RAGE upregulation in proinflammatory environments and the proved increased expression of this receptor in a variety of acute and chronic inflammatory diseases provide support for RAGE as an attractive target for future clinical interventions related to inflammation.

Therefore, several attempts were performed in order to block this extracellular HMGB1 chemo-cytokine protein. Several important approaches were addressed to the administration of antibodies against HMGB1, of HMGB1 fragments (for example HMGB1 A-Box), of antibodies to RAGE, of soluble RAGE (sRAGE) and of ethyl pyruvate (Czura et al., 2003; Lotze et al., 2003).

The passive immunization of mice with HMGB1-neutralizing antibodies conferred a highly significant, dose-dependent and lasting protection against lethal doses of endotoxin, even when the first doses of antibodies were given after the TNF peak had passed, suggesting that antagonizing HMGB1 activity late in the clinical course may be an effective treatment approach to potentially lethal sepsis (Yang et al., 2004).

Another possibility is to administer mono- or oligoclonal antibodies against the HMGB1 B-Box, or its 20 amino acid relevant core which signals through RAGE. Furthermore, HMGB1 A-Box, one of the two DNA-binding domains in HMGB1, has been identified as a specific antagonist of HMGB1: highly purified recombinant A-Box has protected mice from lethal experimental sepsis even when initial treatment has been delayed for 24 hours after pathology induction, further suggesting that HMGB1 antagonists may be administered successfully in a clinically relevant window wider than the one used for other known cytokines (Yang et al., 2004).

Structural function analysis of HMGB1-truncated mutants has revealed that the A-Box domain of HMGB1 competitively displaces the saturable binding of HMGB1 to macrophages, specifically antagonizing HMGB1 activities. As has been already seen with the protective activity of anti-HMGB1 antibodies, the administration of the A-Box rescues mice from sepsis even when treatment has been initiated as late as 24 hours after surgical induction of sepsis (Yang H. et al., 2004). HMGB1 antagonists or inhibitors selected from the group of antibodies or antibody fragments that bind to an HMGB1 protein, HMGB1 gene antisense sequences and HMGB1 receptor antagonists are known from U.S. Pat. No. 6,468,533, WO 02/074337 and US 2003/0144201.

Moreover, saturation of circulating HMGB1 by the administration of sRAGE leads to the block of its activities mediated by cellular RAGE, a result which can also be obtained by inhibiting RAGE itself with the administration of anti-RAGE antibodies.

Furthermore, a similar protective response late in the course of sepsis has been observed by administering ethyl-pyruvate, a stable lipophilic derivative and relatively non-toxic food additive also used as an experimental anti-inflammatory agent, which attenuates the systemic inflammation of ischemia/reperfusion tissue injury and lethal hemorrhagic shock. Ethyl-pyruvate inhibited HMGB1 and TNF release in vitro from endotoxin-stimulated murine macrophages, while in vivo protected mice from peritonitis-induced lethal sepsis, again when dosing was begun 24 hours after this pathology was experimentally induced.

Finally, it has been shown that the N-terminal lectin-like domain (D1) of thrombomodulin is an inhibitor of HMGB1, since it binds to and sequesters this chemokine, preventing the binding of HMGB1 to RAGE and Toll-like receptors such that the downstream cascade of events leading to inflammatory pathologies is inhibited.

As described above, several attempts were performed with the aim of inhibiting and/or antagonising the extracellular HMGB1 chemo-cytokine protein. The present invention is based on the experimental evidence that the two high affinity binding domains for DNA, i.e. HMGB1 Box-A and HMGB1 Box-A, which are present in the HMGB1 molecule, have two opposing roles in the protein released in the extracellular space. The main activity of HMGB1 Box-B is to mediate the pro-inflammatory activities attributed to the HMGB1 protein. On the other hand, HMGB1 Box-A acts as an antagonist competing with the pro-inflammatory activity of the Box-B domain.

The problem underlying the present invention was therefore the provision of novel agents for the prevention, alleviation and/or treatment of HMGB1-associated pathologies. In particular, the problem of the present invention was to develop novel agents as selective extracellular HMGB1 antagonist and/or inhibitors, in order to prevent, alleviate and/or treat the broad spectrum of pathological effects induced by the HMGB1 chemokine itself and/or by the cascade of multiple inflammatory cytokines caused by the extracellular release of the HMGB1 protein.

The inventors of the present invention based their studies on the evidence that HMGB1 Box-A behaves as an antagonist in the pathological conditions induced and/or sustained by HMGB1 and as inhibitors of RAGE. Hence HMGB1 Box-A represents a high potential therapeutic approach to block both the contribution of HMGB1 and of RAGE to inflammatory disorders.

However, the delivery of therapeutic proteins for clinical use is a major challenge to pharmaceutical science. Most natural proteins, as such, are inefficient drugs due to sub-optimal performance in terms of potency, stability, immunogenicity, side effects or toxicity. Once in the blood stream, these proteins are constantly eliminated from circulation within a short time. Different physiological processes involving metabolism as well as clearance through normal pathways of protein elimination (such as glomerular filtration in the kidneys or proteolysis in blood) are involved. Consequently, also the therapeutic use is limited by a very short half-life in plasma.

Hence the need to identify a HMGB1 Box-A variant specifically designed to maintain the same or a higher pharmacological activity of wild type but characterized by a consistent increased resistance to proteases and consequently improved pharmacokinetic and pharmacodynamic performance exists in the art.

The solution to the above problem is therefore the provision of a polypeptide variant of the human and/or non-human HMGB1 high affinity binding domain Box-A (HMGB1 Box-A) or of a biologically active fragment of human and/or non-human HMGB1 Box-A, characterized in that the amino acid sequence of said polypeptide variant differs from the amino acid sequence of the wild type HMGB1 Box-A protein by the mutation of one or more single amino acids. Surprisingly, it was found by the inventors of the present invention that said polypeptide variant exhibits an increased resistance to proteolysis compared to wild type HMGB1 Box-A or to the biological active fragment of the wild type HMGB1 Box-A together with the maintenance of the same or development of even higher pharmacological activity.

By increasing the resistance to the proteolytic activity of the proteases, a more favourable pharmacokinetic and pharmacodynamic profile can be achieved, since an increased stability in body fluids is obtained for the inventive polypeptide variants. As a result thereof, an increase in the half-life in body fluids of the protein's variants of the present invention is observed as well. It is known that the estimated half-life of proteins in vivo can be as short as a few minutes. The variants of the present invention preferably have an increased half-life, e.g. because they are more resistant to proteases.

In a most preferred embodiment of the present invention, polypeptide variants are obtained by using a directed evolution process, which technology is extensively described in WO 2004/7022593 and in several further patent applications (PCT/FR00/03503, PCT/FR01/01366, U.S. Ser. No. 10/022,249, U.S. Ser. No. 10/022,390, U.S. Ser. No. 10/375,192, U.S. 60/409,898, U.S. 60/457,135, U.S. 60/410,258 and U.S. 60/410,263), all in the name of Nautilus Biotech S.A. (Paris, France), which are herein incorporated by reference.

In general, the term “directed evolution” refers to biotechnological processes devoted to the improvement of target protein features by means of specific changes introduced into their amino acid sequences. The directed evolution process includes the generation of a library of mutant versions of the gene of interest, followed by the selection of those variants that display the desired features. These processes can be iterative when gene products having an improvement in a desired property are subjected to further cycles of mutation and screening.

In order to optimise the Box-A of HMGB1 protein and to obtain the polypeptide variants of the present invention with higher stability against proteases, a particular Nautilus proprietary technology for directed evolution has been applied. In particular, a so-called two-dimensional rational mutagenesis scanning approach (“2-D scanning”) has been applied, which is described in the Nautilus patent application WO 2004/022593, said application being herein incorporated by reference.

Nautilus 2-D scanning approach for protein rational evolution is based on a process, in which two dimensions of the target protein are scanned by serial mutagenesis in order to find the right amino acid change that is needed at the right amino acid position. The first dimension that is scanned is the amino acid position along the target protein sequence, in order to identify those specific amino acid residues to be replaced with different amino acids. These amino acid positions are referred to as is-HIT target positions. The second dimension is the specific amino acid type selected for replacing a particular is-HIT target position. According to a particular approach of the 2-D scanning method, a number of target positions along the protein sequence are selected, in silico. As used herein, in silico refers to research and experiments performed using a computer. In this context, in silico methods include, but are not limited to, molecular modeling studies and biomolecular docking experiments. Therefore, the amino acid target positions on the protein sequence are identified without use of experimental biological methods. Once a protein feature to be optimised is selected, diverse sources of information or previous knowledge are exploited in order to determine those amino acid positions that may be amenable to improve the protein's fitness by replacement with a different amino acid. In particular the “is-HIT target positions” are identified based on three factors, being (i) the protein feature to be evolved and optimised, (ii) the protein's amino acid sequence and/or (iii) the known properties of the individual amino acids.

In the specific context of the present invention, the “in silico HITs” (“is-HITs”) are all possible candidate amino acid positions along the target protein's primary sequence that might be involved as target for the proteolytic activity of proteases. Based on the specific list of proteases considered in the context of the present invention (FIG. 1), the complete list of all amino acid sequences that could potentially be targeted within the wild type HMGB1-Box-A amino acid sequence is determined.

Once the is-HIT target positions have been selected, mutagenesis then is performed by the replacement of single amino acid residues at the specific acid target positions on the protein backbone. The mutagenesis is performed by residue replacement “one-by-one” in addressable arrays and molecules containing the preselected amino acid changes at each of the target amino acid positions are produced.

The choice of the replacing amino acid takes into account the need to preserve the physicochemical properties such as hydrophobicity, charge and/or polarity of essential residues (such as catalytic and binding residues). Numerous methods of selecting replacing amino acids are well known in the art, in particular, amino acid substitution matrixes are used for this purpose. A very preferred technology according to the present invention makes use of the so-called “Percent Accepted Mutation” (PAM) (Dayhoff et al., Atlas of protein sequence and structure, 5(3):345-352, 1978), as shown in FIG. 2. PAM values are used in order to select an appropriate group of replacement amino acids. PAM values, originally developed to produce alignments between protein sequences, are available in the form of probability matrixes, which reflect an evolutionary distance. “Conservative substitutions” of a residue in a reference sequence are those substitutions that are physically and functionally similar to the corresponding reference residues, e.g. those that have a similar size, shape, electric charge, chemical properties, including the ability to form covalent or hydrogen bonds, or the like. Preferred conservative substitutions show the highest scores fitting with the PAM matrix criteria in the form of “accepted point mutations”. The PAM250 matrix is used in 2-D scanning to identify the replacing amino acids for the is-HITs in order to generate conservative mutations without affecting the protein function. At least, the two amino acids with the highest values in PAM250 matrix, corresponding to “conservative substitutions” or “accepted point mutations”, are chosen. The replacement of amino acids by cysteine residues is explicitly avoided, since this change would potentially lead to the formation of intermolecular disulfide bonds.

Using the above-resumed Nautilus Biotech directed evolution technology, the inventors of the present application were able to obtain polypeptide variants of the HMGB1 Box-A which differ from the amino acid sequence of the native target polypeptide by one or more mutation.

In the context of the present invention, where reference is made to the term “HMGB1 Box-A or amino acid sequence of HMGB1 Box-A”, it is referred to both human and non-human HMGB1 Box-A. In a preferred embodiment of the present invention, the systematic mutation of single amino acid on the critical is-HITs positions for proteases has been obtained on the wild type of human HMGB1 Box-A protein and on the wild type of Anopheles gambia HMGB1 Box-A protein. The choice of the species Anopheles gambia was made by the inventors of the present application after a proper structural and phylogenetic analysis showing a 68% identity and a 88% homology of the human and Anopheles HMGB1 Box-A.

“Biologically active fragments of HMGB1 Box-A” as used herein are meant to encompass parts of the known wild type HMGB1 Box-A protein, for which at least one of the biological activities of the corresponding mature protein is still observable when known tests are being used. Preferably, a fragment of the mature protein is considered as biologically active if an antagonist activity with respect to the pro-inflammatory activity of the HMGB1 B-Box and the HMGB1 protein as a whole can be determined. Biologically active fragments of native HMGB1 Box-A are fragments of at least 20, 25, 30, 35, 45, 50, 55, 60, 65, 70, 75 or 80 amino acids. Preferred biologically active fragments of native HMGB1 Box-A used in the context of the present invention comprises fragments of at least 77 or of at least 54 amino acids, respectively.

The term “mutation” as used in the context of the present invention can be understood as substitution, deletion and/or addition of single amino acid in the target sequence. Preferably, the mutation of the target sequence in the present invention is a substitution. The substitution can occur with different genetically encoded amino acid or by non-genetically encoded amino acids. Examples for non-genetically encoded amino acids are homocystein, hydroxyproline, ornithin, hydroxylysine, citrulline, carnitine, etc.

The polypeptide variants of the present invention obtained by using directed evolution technology are mutant proteins which differ from the amino acid sequence of the wild type HMGB1 Box-A by the mutation of one or more single amino acid. In a very preferred embodiment of the present invention, only one amino acid replacement occurs on the sequence of the native protein. In this case, the polypeptide variant of the invention is obtained by the modification of the native protein, such that the amino acid sequence of the variant differs from that of the native protein by a single amino acid change at only one of the is-HIT target positions. It is, however, encompassed by the subject of the present invention that the native protein can be further optimised by replacement of a plurality, e.g two or more, of is-HIT target positions on the same protein molecule. According to this variant of the invention, polypeptide variants are obtained by combining the single mutation into a single protein molecule. The modified polypeptide variants having more single amino acid replacement can differ from the wild type protein sequence by amino acid replacements on 1-10, preferably 2, 3, 4, 5 and 6 different amino acid target positions.

The selection of the candidate lead of the series of polypeptide variants produced with the technology used in the present invention is based both on the more favourable pharmacokinetic profile, obtained thanks to the longer resistance to proteases and on a better pharmacodynamic profile thanks to an increased intrinsic activity and binding affinity which gives a greater antagonistic activity than the native HMGB1 Box-A protein.

In a particular embodiment of the invention, starting from Human HMGB1 Box-A as starting native protein, three groups of polypeptide variants are obtained. In particular, one group of polypeptide variants is derived from single mutations introduced into the full-length amino acid sequence (84 amino acids) from Human HMGB1 Box-A (SEQ ID NO:1). The other two groups of inventive polypeptide variants are generated starting from biologically active fragments of Human HMGB1 Box-A of 77 amino acids (SEQ ID NO:117) and 54 amino acids (SEQ ID NO:223), respectively.

In a further particular embodiment of the invention, starting from Anopheles gambia HMGB1 Box-A as starting native protein, three groups of polypeptide variants are obtained. In particular, one group of polypeptide variants is derived from single mutations introduced into the full-length amino acid sequence (84 amino acids) from Anopheles gambia HMGB1 Box-A (SEQ ID NO:301). The other two groups of inventive polypeptide variants are generated starting from biologically active fragments of Anopheles gambia HMGB1 Box-A of 77 amino acids (SEQ ID NO:419) and 54 amino acids (SEQ ID NO:529), respectively.

Hence, the above-mentioned very preferred polypeptide variants of this invention are defined as below.

1) On the human HMGB1 Box-A full-length fragment of 84 amino acids defined by the sequence SEQ ID NO:1 (FIG. 3 a), 53 amino acid positions, recognized as substrate for different proteases (cf. FIG. 1), are identified. The numbering corresponds to that in the wild type protein:

K2, D4, P5, K6, K7, P8, R9, K11, M12, Y15, F17, F18, R23, E24, E25, K27, K28, K29, P31, D32, F37, E39, F40, K42, K43, E46, R47, W48, K49, M51, K54, E55, K56, K58, F59, E60, D61, M62, K64, D66, K67, R69, Y70, E71, R72, E73, M74, K75, Y77, P79, P80, K81, E83.

The native amino acid at each of these positions is replaced by residues defined by the substitution matrix PAM250 (cf. FIG. 2). In particular, the performed residue substitutions are as listed below.

R to H, Q

E to H, Q, N

K to Q, T

D to N, Q

M to I, V

P to A, S

Y to I, H

F to I, V

W to Y, S

A total of 115 polypeptide variants of Box-A of human HMGB1 are generated (FIG. 3 a). These polypeptide variants are defined in sequences SEQ ID NOs:2 to 116.

2) On the Human HMGB1 Box-A biologically active fragment of 77 amino acids, defined in sequence SEQ ID NO:117 (FIG. 4 a), 48 amino acid positions, recognized as substrate for different proteases (cf. FIG. 1), are identified. The numbering is in accordance to their position in SEQ ID NO:117:

P1, R2, K4, M5, Y8, F10, F11, R16, E17, E18, K20, K21, K22, P24, D25, F30, E32, F33, K35, K36, E39, R40, W41, K42, M44, K47, E48, K49, K51, F52, E53, D54, M55, K56, D59, K60, R62, Y63, E64, R65, E66, M67, K68, Y70, P72, P73, K74, E76.

The native amino acid in each of these positions is replaced by residues defined by the substitution matrix PAM250 (cf. FIG. 2). In particular, the performed residue substitutions are as listed below.

R to H, Q

E to H, Q, N

K to Q, T

D to N, Q

M to I, V

P to A, S

Y to I, H

F to I, V

W to Y, S

A total of 105 polypeptide variants of Box-A of human HMGB1 fragment of 77 amino acids are generated (FIG. 4 b) and defined as in sequences SEQ ID NOs:118 to 222.

3) On the Human HMGB1 Box-A biologically active fragment of 54 amino acids defined in sequence SEQ ID NO:223 (FIG. 5 a), 35 amino acid positions, recognized as substrate for different proteases (FIG. 1), are identified. The numbering is in accordance to their position in SEQ ID NO:223:

P1, D2, F7, E9, F10, K12, K13, E16, R17, W18, K19, M21, K24, E25, K26, K28, F29, E30, D31, M32, K34, D36, K37, R39, Y40, E41, R42, E43, M44, K45, Y47, P49, P50, K51, E53.

The native amino acid at each of these positions is replaced by residues defined by the substitution matrix PAM250 (cf. FIG. 2). In particular, the performed residue substitutions are as listed below.

R to H, Q

E to H, Q, N

K to Q, T

D to N, Q

M to I, V

P to A, S

Y to I, H

F to I, V

W to Y, S

A total of 77 polypeptide variants of Box-A of human HMGB1 fragment of 54 amino acids are generated (FIG. 5 b) and defined as in sequences SEQ ID NOs:224 to 300.

4) On the Anopheles gambia (XP_(—)311154) HMGB1 Box-A full-length fragment of 84 amino acids, defined by the sequence SEQ ID NO:301 (FIG. 6 a), 53 amino acid positions, recognized as substrate for different proteases (FIG. 1), were identified. The numbering is in accordance with the position in the native protein.

K2, K4, D5, K7, P8, R9, R11, M12, Y15, F17, F18, R23, E24, E25, K27, K28, K29, P31, E32, E33, F37, E39, F40, R42, K43, E46, R47, W48, K49, M51, L52, D53, K54, E55, K56, R58, F59, E61, M62, E64, K65, D66, K67, R69, Y70, E71, L72, E73, M74, Y77, P79, P80, K81.

The native amino acid at each of these positions was replaced by residues defined by the substitution matrix PAM250 (cf. FIG. 2).

The performed actual residue substitutions are as listed below.

R to H, Q

E to H, Q, N

K to Q, T

D to N, Q

M to I, V

P to A, S

Y to I, H

F to I, V

W to Y, S

A total of 117 variants of Box-A of HMGB1 Anopheles gambia (XP_(—)311154) were generated (FIG. 6 b) and identified in the sequences as defined in SEQ ID NOs:302 to 418.

5) On the Anopheles gambia (XP_(—)311154) HMGB1 Box-A biologically active fragment of 77 amino acids, defined in sequence SEQ ID NO:419 (FIG. 7 a), 49 amino acid positions, recognized as substrate for different proteases (cf. FIG. 1), were identified. The numbering is in accordance with the position in the sequence as defined in SEQ ID NO:419.

P1, R2, R4, M5, Y8, F10, F11, R16, E17, E18, K20, K21, K22, P24, E25, E26, F30, E32, F33, R35, K36, E39, R40, W41, K42, M44, L45, D46, K47, E48, K49, R51, F52, E54, M55, E57, K58, D59, K60, R62, Y63, E64, L65, E66, M67, Y70, P72, P73, K74.

The native amino acid at each of these positions was replaced by residues defined by the substitution matrix PAM250 (cf. FIG. 2).

The performed actual residue substitutions are as listed below.

R to H, Q

E to H, Q, N

K to Q, T

D to N, Q

M to I, V

P to A, S

Y to I, H

F to I, V

W to Y, S

A total of 109 polypeptide variants of Box-A of HMGB1 fragment of 77 amino acids were generated (FIG. 7 b) and identified as defined in sequences SEQ ID NOs:420 to 528.

6) On the Anopheles gambia (XP_(—)311154) HMGB1 Box-A biologically active fragment of 54 amino acids defined in sequence SEQ ID NO:529 (FIG. 8 a), 36 amino acid positions, recognized as substrate for different proteases (cf. FIG. 1), were identified. The numbering is in accordance with the position on the sequence as defined in SEQ ID NO:529.

P1, E2, E3, F7, E9, F10, R12, K13, E16, R17, W18, K19, M21, L22, D23, K24, E25, K26, R28, F29, E31, M32, E34, K35, D36, K37, R39, Y40, E41, L42, E43, M44, Y47, P49, P50, K51.

The native amino acid in each of these positions was replaced by residues defined by the substitution matrix PAM250 (cf. FIG. 2).

The performed actual residue substitutions are as listed below.

R to H, Q

E to H, Q, N

K to Q, T

D to N, Q

M to I, V

P to A, S

Y to I, H

F to I, V

W to Y, S

A total of 81 polypeptide variants of Box-A of HMGB1 Anopheles gambia (XP_(—)311154) fragment of 54 amino acids were generated (FIG. 8 b) and identified in the sequences as defined in SEQ ID NOs:530 to 610.

It is noted that the amino acids which occur in the various amino acid sequences appearing herein are identified according to their known one-letter code abbreviations. It should be further noted that all amino acid residue sequences represented herein by their one-letter abbreviation code have a left-to-right orientation in the conventional direction of amino-terminus to carboxyl-terminus.

Accordingly, the present invention provides modified polypeptide variants that exhibit increased resistance to the proteolytic activity of proteases and/or peptidases compared to the wild type HMGB1 Box-A protein together with a similar or even higher antagonistic activity than the native HMGB1 Box-A protein. The polypeptide variants of the invention in particular exhibit an increase in the resistance to the proteolytic activity of the human proteases and/or peptidases, in particular of the human serum proteases and/or human gastro-intestinal proteases or peptidases. Preferred proteases are listed in FIG. 1. In a more preferred embodiment of the invention, polypeptide variants exhibit an increase in the resistance to the proteolytic activity of at least a protease selected from the group comprising chymotrypsin, trypsin, endoprotease, endopeptidases or a combination thereof.

In particular, the resistance to proteolysis is at least 10%, 20%, 30%, 40%, 50%, 70%, 80%, 90%, 95% or higher compared to the unmodified wild type HMGB1 Box-A. Protease resistance was measured at different timepoints (between 5 minutes and 8 hours) at 25° C. after incubation of 20 μg of Box-A wild type or variants with a mixture of proteases at 1% w/w of total proteins. The mixture of the proteases was prepared freshly at each assay from stock solutions of endoproteinase Glu-C (SIGMA) 200 μg/ml; trypsin (SIGMA) 400 μg/ml and α-chymotrypsin (SIGMA) 400 μg/ml. After protease incubation the reaction was stopped adding 10 μl of anti-proteases solution (Roche) and the samples were stored at −20° C. for the biological activity assay.

In particular, in order to identify the most preferred polypeptide variants of the invention, studies have been conducted to determine the variants which show both a similar or even improved activity and an increased protease resistance compared to the wild-type HMGB1 Box-A protein. For this purpose, the activity of Box-A polypeptide variants of human HMGB1 Box-A full-length fragment in inhibiting HMGB1-induced NIH/3T3 cell migration was determined in chemotaxis assays in comparison to Box-A wild-type (Example 6 and FIGS. 12A to 12R). Moreover for the polypeptide variants, which show a similar or even higher antagonistic activity than the native HMGB1 Box-A protein of SEQ ID NO:1 the in vitro resistance to protease digestion was determined by incubation of each of these polypeptide variants with a mixture of trypsin, α-chymotrypsin, endoproteinase Asp-N and endoproteinase Glu-C (sigma). This protease resistance test is described in Example 7 and the results of protease resistance profile of said variants are shown in FIGS. 14 to 81.

From the results it can be gathered that the preferred polypeptide variants of the present invention are those variants which show a similar or higher antagonistic activity together with an increased protease resistance. In particular, the preferred polypeptide variants are the polypeptides of SEQ ID NOs: 33, 35, 37-39, 42-45, 47-49, 52, 55, 57, 59, 62, 64, 67, 69 and 104. Among these preferred polypeptide variants, the most preferred variants are those defined in SEQ ID Nos:45, 49, 52, 55, 59, 64 and 67. These very preferred polypeptide variants show a dramatically improved proteinase resistance profile compared with the wild-type human HMGB1 Box-A of SEQ ID NO:1 (cf. results of Example 7).

As a consequence of the increased stability due to the increased resistance to proteases activity, the polypeptide variants of the present invention also exhibit a longer half-life in body fluids compared to the wild type HMGB1 Box-A. In particular, the half-life in serum and/or in blood is increased, whereby an increase of at least 10 minutes, 20 minutes, 30 minutes, 60 minutes or even longer, compared to the wild type HMGB1 Box-A is observed.

A further aspect of the present invention is a nucleic acid molecule encoding a polypeptide variant of the present invention. In particular, the present invention refers to nucleic acid molecules encoding polypeptide variants as defined in SEQ ID NO:2 to 116, 118 to 222, 224 to 300, 302 to 418, 420 to 528 and 530 to 610. Even more preferably, the present invention refers to nucleic acid molecules encoding for the preferred polypeptide variants as defined above.

A still further aspect of the present invention is a vector comprising a nucleic acid molecule as defined above.

Furthermore, the present invention refers to a method for producing a polypeptide variant as described above comprising (i) introducing a nucleic acid molecule as defined above into a host cell and (ii) culturing the cell, under conditions in which the encoded polypeptide variant is expressed. Preferably the host cell is a mammalian, insect or bacterial cell, in particular E. Coli, preferably the M15 strain.

A further method for producing a polypeptide variant as described above is the use of chemical peptide synthesis, e.g. a solid phase peptide synthesis according to standard methods.

The polypeptide variants of the present invention exhibit an increased resistance to proteolysis and thus a higher stability compared to the unmodified wild type protein. Consequently, the peptides of the invention also exhibit improved therapeutic and biological properties and activity. In fact, they show a more favorable pharmacokinetic and pharmacodynamic profile than native HMGB1 Box-A.

The invention is therefore directed to the use of the above-mentioned polypeptide variants of HMGB1 Box-A, obtained through systematic mutations of single amino acids in the sequence of HMGB1 Box-A or of its biologically active fragments as active agent in a medicament. In a preferred embodiment, the present invention refers to the use of the preferred polypeptide variants as defined above as active agent in a medicament.

A still further aspect of the invention is hence the use of the inventive polypeptide variants, in particular of the preferred polypeptide variants of the present invention as defined above, for the manufacture of a medicament for the prevention and/or treatment of extracellular HMGB1-associated pathologies or pathologies associated with the HMGB1 homologous proteins. In particular, the HMGB1 associated pathologies are pathologies which are mediated by a multiple inflammatory cytokine cascade.

The broad spectrum of pathological conditions induced by the HMGB1-chemokine and by the HMGB1-induced cascade of inflammatory cytokines are grouped in the following categories: inflammatory disease, autoimmune disease, systemic inflammatory response syndrome, reperfusion injury after organ transplantation, cardiovascular affections, obstetric and gynecologic disease, infectious (viral and bacterial) disease, allergic and atopic disease, solid and liquid tumor pathologies, transplant rejection diseases, congenital diseases, dermatological diseases, neurological diseases, cachexia, renal diseases, iatrogenic intoxication conditions, metabolic and iodiopathic diseases.

HMGB1-associated pathologies according to the present invention are preferably pathological conditions mediated by activation of the inflammatory cytokine cascade. Non limiting examples of conditions which can be usefully treated using the present invention include the broad spectrum of pathological conditions induced by the HMGB1-chemokine and by the HMGB1-induced cascade of inflammatory cytokines grouped in the following categories: restenosis and other cardiovascular diseases, reperfusion injury, inflammation diseases such as inflammatory bowel disease, systemic inflammation response syndrome, e.g. sepsis, adult respiratory distress syndrome, etc, autoimmune diseases such as rheumatoid arthritis and osteoarthritis, obstetric and gynaecological diseases, infectious diseases, atopic diseases, such as asthma, eczema, etc, tumor pathologies, e.g. solid or non-solid tumor diseases associated with organ or tissue transplants, such as reperfusion injuries after organ transplantation, organ rejection and graft-versus-host disease, congenital diseases, dermatological diseases such as psoriasis or alopecia, neurological diseases, ophthalmological diseases, renal, metabolic or idiopathic diseases and intoxication conditions, e.g. iatrogenic toxicity, wherein the above diseases are caused by, associated with and/or accompanied by HMGB1 protein release.

In particular, the pathologies belonging to inflammatory and autoimmune diseases include rheumatoid arthritis/seronegative arthropathies, osteoarthritis, inflammatory bowel disease, Crohn's disease, intestinal infarction, systemic lupus erythematosus, iridoeyelitis/uveitis, optic neuritis, idiopathic pulmonary fibrosis, systemic vasculitis/Wegener's granulomatosis, sarcoidosis, orchitis/vasectomy reversal procedures, systemic sclerosis and scleroderma. Systemic sclerosis and scleroderma systemic inflammatory response includes sepsis syndrome (including gram positive sepsis, gram negative sepsis, culture negative sepsis, fungal sepsis, neutropenic fever, urosepsis, septic conjunctivitis), meningococcemia, trauma hemorrhage, hums, ionizing radiation exposure, acute and chronic prostatitis, acute and chronic pancreatitis, appendicitis, peptic, gastric and duodenal ulcers, peritonitis, ulcerative, pseudomembranous, acute and ischemic cholitis, diverticulitis, achalasia, cholangitis, cholecystitis, enteritis, adult respiratory distress syndrome (ARDS). Reperfusion injury includes post-pump syndrome and ischemia-reperfusion injury. Cardiovascular disease includes cardiac stun syndrome, myocardial infarction and ischemia, atherosclerosis, thrombophlebitis, endocarditis, pericarditis, congestive heart failure and restenosis. Obstetric and gynecologic diseases include premature labour, endometriosis, miscarriage, vaginitis and infertility. Infectious diseases include HIV infection/HIV neuropathy, meningitis, B- and C-hepatitis, herpes simplex infection, septic arthritis, peritonitis, E. coli 0157:H7, pneumonia epiglottitis, haemolytic uremic syndrome/thrombolytic thrombocytopenic purpura, candidiasis, filariasis, amebiasis, malaria, Dengue hemorrhagic fever, leishmaniasis, leprosy, toxic shock syndrome, streptococcal myositis, gas gangrene, mycobacterium tuberculosis, mycobacterium avium intracellulare, pneumocystis carinii pneumonia, pelvic inflammatory disease, orchitis/epidydimitis, legionella, Lyme disease, influenza A, Epstein-Barr Virus, Cytomegalovirus, viral associated hemiaphagocytic syndrome, viral encephalitis/aseptic meningitis. Allergic and atopic disease include asthma, allergy, anaphylactic shock, immune complex disease, hay fever, allergic rhinitis, eczema, allergic contact dermatitis, allergic conjunctivitis, hypersensitivity pneumonitis. Malignancies (liquid and solid tumor pathologies) include ALL, AML, CML, CLL, Hodgkin's disease, non Hodgkin's lymphoma, Kaposi's sarcoma, colorectal carcinoma, nasopharyngeal carcinoma, malignant histiocytosis and paraneoplastic syndrome/hypercalcemia of malignancy. Transplant diseases include organ transplant rejection and graft-versus-host disease. Congenital disease includes cystic fibrosis, familial hematophagocytic lymphohistiocytosis and sickle cell anemia. Dermatologic disease includes psoriasis, psoriatic arthritis and alopecia. Neurologic disease includes neurodegenerative diseases (multiple sclerosis, migraine, headache, amyloid-associated pathologies, prion diseases/Creutzfeld-Jacob disease, Alzheimer and Parkinson's diseases, multiple sclerosis, amyotrophic emilateral sclerosis) and peripheral neuropathies, migraine, headache. Renal disease includes nephrotic syndrome, hemodialysis and uremia. Iatrogenic intoxication condition includes OKT3 therapy, Anti-CD3 therapy, Cytokine therapy, Chemotherapy, Radiation therapy and chronic salicylate intoxication. Metabolic and idiopathic disease includes Wilson's disease, hemochromatosis, antitrypsin deficiency, diabetes and diabetes complications, weight loss, anorexia, cachexia, obesity, Hashimoto's thyroiditis, osteoporosis, hypothalamic-pituitary-adrenal axis evaluation and primary biliary cirrhosis. Ophtalmological disease include glaucoma, retinopathies and dry-eye. A miscellanea of other pathologies comprehends: multiple organ dysfunction syndrome, muscular dystrophy, septic meningitis, atherosclerosis, epiglottitis, Whipple's disease, asthma, allergy, allergic rhinitis, organ necrosis, fever, septicaemia, endotoxic shock, hyperpyrexia, eosinophilic granuloma, granulomatosis, sarcoidosis, septic abortion, urethritis, emphysema, rhinitis, alveolitis, bronchiolitis, pharyngitis, epithelial barrier dysfunctions, pneumoultramicropicsilicovolcanoconiosis, pleurisy, sinusitis, influenza, respiratory syncytial virus infection, disseminated bacteremia, hydatid cyst, dermatomyositis, burns, sunburn, urticaria, warst, wheal, vasulitis, angiitis, myocarditis, arteritis, periarteritis nodosa, rheumatic fever, celiac disease, encephalitis, cerebral embolism, Guillame-Barre syndrome, neuritis, neuralgia, iatrogenic complications/peripheral nerve lesions, spinal cord injury, paralysis, uveitis, arthriditis, arthralgias, osteomyelitis, fasciitis, Paget's disease, gout, periodontal disease, synovitis, myasthenia gravis, Goodpasture's syndrome, Babcets's syndrome, ankylosing spondylitis, Barger's disease, Retier's syndrome, bullous dermatitis (bullous pemphigoid), pemphigous and pemphigous vulgaris and alopecia.

In a further aspect of the invention, the use of the polypeptide variants obtained through systematic mutations of amino acid sequences of human and non-human Box-A of HMGB1, or of its biologically relevant fragments described above, is in combination with a further agent.

The further agent is preferably an agent capable of inhibiting an early mediator of the inflammatory cytokine cascade. Preferably, this further agent is an antagonist or inhibitor of a cytokine selected from the group consisting of TNF, IL-1α, IL-1β, IL-Ra, IL-6, IL-8, IL-10, IL 13, IL-18, IFN-γ MIP-1α, MIF-1β, MIP-2, MIF and PAF.

The further agent used in combination with the polypeptide variants of HMGB1 Box-A, or of its biologically relevant fragments, may also be an inhibitor of RAGE, e.g. an antibody directed to RAGE, a nucleic acid or nucleic acid analogue capable of inhibiting RAGE expression, e.g. an antisense molecule, a ribozyme or a RNA interference molecule, or a small synthetic molecule antagonist of the interaction of HMGB1 with RAGE, preferably of the interaction of the non-acetylated or/and acetylated form of HMGB1 with RAGE, or soluble RAGE (sRAGE). The antibody to RAGE is preferably a monoclonal antibody, more preferably a chimeric or humanised antibody or a recombinant antibody, such as a single chain antibody or an antigen-binding fragment of such an antibody. The soluble RAGE analog may be optionally present as a fusion protein, e.g. with the Fc domain of a human antibody. The small synthetic molecular antagonist of the HMGB1 interaction with RAGE preferably has a molecular weight of less than 1000 Dalton. The small synthetic molecular antagonist preferably inhibits the interaction of RAGE with the non-acetylated form or/and with the acetylated form of HMGB1 and with the non-acetylated form or/and with the acetylated form of HMGB1 homologous proteins, particularly HMGB2, HMGB3, HMG-1L10, HMG-4L or/and SP100-HMG.

The further agent used in combination with the polypeptide variants of HMGB1 Box-A, or of its biologically relevant fragments, may also be an inhibitor of the interaction of a Toll-like receptor (TLR), e.g. of TLR2, TLR4, TLR7, TLR8 or/and TLR9, with HMGB1, which inhibitor is preferably a monoclonal or polyclonal antibody, a nucleic acid or nucleic acid analogue capable of inhibiting TLR expression, e.g. an antisense molecule, a ribozyme or a RNA interference molecule, or a synthetic molecule preferably having a size of less than 1000 Dalton. The inhibitor may be a known inhibitor of a Toll-like receptor, in particular of TLR2, TLR4, TLR7, TLR8 or/and TLR9. The inhibitor preferably inhibits the interaction of the Toll-like receptor with the non-acetylated form or/and the acetylated form of HMGB1 and with the non-acetylated form or/and with the acetylated form of HMGB1 homologous proteins, in particular HMGB2, HMGB3, HMG-1L10, HMG-4L or/and SP100-HMG.

In still another embodiment, the further agent used in combination with the polypeptide variants of HMGB1 Box-A, or of its biologically relevant fragments, is the functional N-terminal lectin-like domain (D1) of thrombomodulin. The D1 domain of thrombomodulin is able to intercept the non-acetylated form and/or the acetylated form of released HMGB1 and of released HMGB1 homologous proteins, in particular HMGB2, HMGB3, HMG-1L10, HMG-4L or/and SP100-HMG, preventing thus their interaction with RAGE and Toll-like receptors. The D1 domain of thrombomodulin may be native or mutated in order to make it resistant to proteases.

The further agent may also be a synthetic double-stranded nucleic acid or nucleic acid analogue molecule with a bent shape structure, particularly a double-stranded bent DNA, PNA or DNA/PNA chimera or hybrid or a double-stranded cruciform DNA, PNA or DNA/PNA chimera or hybrid structure, capable of binding to the HMGB1 protein. Preferred nucleic acids and nucleic analogue molecules are disclosed in a co-owned and co-pending international patent application No. PCT/EP2005/007198 filed on 4 Jul. 2005 (claiming the priority of U.S. provisional application No. 60/584,678 filed on 2 Jul. 2004), which are incorporated herein by reference. The synthetic double-stranded nucleic acid or nucleic acid analogue molecule with a bent shape structure is preferably capable of binding to the non-acetylated or/and to the acetylated form of HMGB1 and the non-acetylated or/and the acetylated form of HMGB1 homologous proteins, in particular HMGB2, HMGB3, HMG-1L10, HMG4L or/and SP100-HMG.

In a still further embodiment, the further agent used in combination with the inventive polypeptide variants is K-252a or/and a salt or derivative thereof or a polymer conjugate of K-252a or/and of a derivative thereof. The use of K-252a or polymer conjugate of K-252a and derivatives thereof is disclosed in a co-owned and co-pending international patent application No. PCT/EP2005/008258 and US provisional application filed on 25 Aug. 2005.

Therefore, a further aspect of the present invention is a pharmaceutical composition comprising an effective amount of at least one of the polypeptide variants of HMGB1 Box-A or a biologically active fragment thereof in particular of the preferred polypeptide variants of the invention as defined above as an active ingredient for the treatment of HMGB1-associated pathologies and pharmaceutically acceptable carriers, diluents and/or adjuvants. The pharmaceutical composition of the present invention is preferably suitable for the treatment of pathologies associated with the non-acetylated or/and the acetylated form of HMGB1 and/or of HMGB1 homologous proteins. In a further preferred embodiment, the pharmaceutical composition of the present invention comprising the at least one polypeptide variant also comprises a further agent as defined above. The pharmaceutical composition of the present invention may be used for diagnostic or for therapeutic applications.

The exact formulation, route of administration and dosage can be chosen by the individual physician in view of the patient's conditions. Administration may be achieved in a single dose or repeated doses at intervals. Dosage amount and interval may be adjusted individually in order to provide the therapeutical effect which results in amelioration of symptoms or a prolongation of the survival in a patient. The actual amount of composition administered will, of course, be dependent on the subject being treated, on the subject's weight, the severity of the affliction, the manner of administration and the judgement of the prescribing physician. A suitable daily dosage will be between 0.001 to 10 mg/kg, particularly 0.1 to 5 mg/kg.

The administration may be carried out by known methods, e.g. by injection, in particular by intravenous, intramuscular, transmucosal, subcutaneous or intraperitoneal injection and/or by oral, topical, nasal, inhalation, aerosol and/or rectal application, etc. The administration may be local or systemic.

In addition, the variants of Box-A of HMGB1, or of its pharmacologically active fragments, object of this invention can be reversibly immobilized and/or adsorbed on the surface and/or inside medical devices or drug release/vehicling systems (microspheres). Medical devices and microspheres can be reversibly loaded with the polypeptide variants of Box-A object of this invention, through their binding, impregnation and/or adsorption on the surface of the medical device or of the microsphere or on a layer that coats its surface. When the medical device or the microsphere come into contact with biological fluids, the reversibly immobilized variant of Box-A is released. Therefore, the medical device and the microsphere act as drug-releasing tools that elute the molecule object of this invention in such a way that their release kinetics can be controlled, ensuring controlled or sustained release, as required by the treatment. The methods for coating/impregnating the medical devices and loading microspheres are well known by experts in these technologies.

Thus, a further aspect of this invention is the way of using the variants of Box-A of HMGB1 or its pharmacologically relevant fragments, wherein the mutated polypeptide molecules are reversibly immobilized on the surface of medical devices or of microspheres or are adsorbed within them. These medical instruments are preferably surgical tools, implants, catheters or stents, for example stents for angioplasty and, in particular, medicated drug-eluting stents.

Another aspect of the invention concerns a medical device reversibly coated with at least one polypeptide variant of the invention. Such a device can be selected from surgical instruments, implants, catheters or stents. Such a device may be useful for angioplasty.

The invention is further illustrated by the following Figures and Examples. The examples are intended to exemplify generic processes and are included for illustrative purpose only, without intention of limiting the scope of the present invention.

FIG. 1 shows the proteases used for the in silico identification of the amino acid positions (is-HITs) on the HMGB1 Box-A amino acid sequence which are targets for the proteolytic activity.

FIG. 2 depicts the “Percent Accepted Mutation” (PAM 250) matrix. Values given to identical residues are shown in grey square. Highest values in the matrix are shown in black square and correspond to the highest occurrence of substitution between two residues.

FIG. 3 a displays the amino acid sequence of the native Human HMGB1 Box-A made of 84 amino acid residues [SEQ ID NO: 1]. In bold, the amino acids sensitive to proteases proteolysis are identified, showing the is-HIT residue positions.

FIG. 3 b shows the type of replacing amino acids on the respective is-HITs target positions selected to generate the polypeptide variant of the full-length human HMGB1 Box-A. Further, the specific amino acid sequences of the generated polypeptide variant are displayed in SEQ ID NOs:2 to 116.

FIG. 4 a displays the amino acid sequence of the biologically active fragment of Human HGB1 Box-A made of 77 amino acid residues [SEQ ID NO: 117]. In bold, the amino acids sensitive to proteases proteolysis are identified, showing the is-HIT residue positions.

FIG. 4 b shows the type of replacing amino acids on the respective is-HITs target positions selected to generate the polypeptide variant of the biologically active fragment of Human HMGB1 Box-A made of 77 amino acid residues. Further the specific amino acid sequences of the generated polypeptide variant are displayed in SEQ ID NOs: 118 to 222.

FIG. 5 a displays the amino acid sequence of the biologically active fragment of Human HMGB1 Box-A made of 54 amino acid residues [SEQ ID NO: 223]. In bold, the amino acids sensitive to proteases proteolysis are identified, showing the is-HIT residue positions.

FIG. 5 b shows the type of replacing amino acids on the respective is-HITs target positions selected to generate the polypeptide variant of the biologically active fragment of Human HMGB1 Box-A made of 54 amino acid residues. Further, the specific amino acid sequences of the generated polypeptide variant are displayed in SEQ ID NOs: 224 to 300.

FIG. 6 a displays the amino acid sequence of the native Anopheles gambia HMGB1 Box-A made of 84 amino acid residues [SEQ ID NO: 301]. In bold, the amino acids sensitive to proteases proteolysis are identified, showing the is-HIT residue positions.

FIG. 6 b shows the type of replacing amino acids on the respective is-HITs target positions selected to generate the polypeptide variant of the full-length Anopheles gambia HMGB1 Box-A. Further, the specific amino acid sequences of the generated polypeptide variant are displayed in SEQ ID NOs: 302 to 418.

FIG. 7 a displays the amino acid sequence of the biologically active fragment of Anopheles gambia HMGB1 Box-A made of 77 amino acid residues [SEQ ID NO: 419]. In bold, the amino acids sensitive to proteases proteolysis are identified, showing the is-HIT residue positions.

FIG. 7 b shows the type of replacing amino acids on the respective is-HITs target positions selected to generate the polypeptide variant of the biologically active fragment of Anopheles gambia HMGB1 Box-A made of 77 amino acid residues. Further the specific amino acid sequences of the generated polypeptide variant are displayed in SEQ ID NOs: 420 to 528.

FIG. 8 a displays the amino acid sequence of the biologically active fragment of Anopheles gambia HMGB1 Box-A made of 54 amino acid residues [SEQ ID NO: 529]. In bold, the amino acids sensitive to proteases proteolysis are identified, showing the is-HIT residue positions.

FIG. 8 b shows the type of replacing amino acids on the respective is-HITs target positions selected to generate the polypeptide variant of the biologically active fragment of Anopheles gambia HMGB1 Box-A made of 54 amino acid residues. Further, the specific amino acid sequences of the generated polypeptide variant are displayed in SEQ ID NOs: 530 to 610.

FIG. 9 shows the plasmid vector containing the nucleic acid sequence encoding for the polypeptide variant of the present invention. The plasmid contains the gene encoding for the polypeptide variant of the present invention, which is under control of the IPTG inducible T5 promoter. The plasmid further contains an ampicillin resistant gene, a 6×His-tag and several restriction sites.

FIG. 10 shows a graph displaying the correlation between the TNF-alpha release induced by the stimulation of HMGB1 in RAW 264.7 cells.

FIG. 11 displays a dose-dependent inhibition of HMGB1-induced TNF-alpha release by a Box-A His-tagged protein.

FIGS. 12A to 12R show the results of the chemotaxis assay described of Example 6 performed on the HMGB1 Box-A polypeptide variants of SEQ ID NO:2 to SEQ ID NO:116 of the present invention. In each figure the activity of a set of polypeptide variants is tested compared to the activity of human wild-type HMGB1 Box-A full-length fragment of SEQ ID NO:1 in the inhibition of HMGB1 induced NIH/3T3 cell migration. Each figure shows a table reporting the statistical analysis numerical data and a column bar graph showing the chemotaxis assay results.

FIGS. 12A and 12B show the bar graph and statistical data of chemotaxis migration assay results in the inhibition of HMGB1-induced NIH/3T3 cells by human HMGB1 Box-A wild type of SEQ ID NO:1 (CT500) and polypeptide variants of SEQ ID NO:2 to 15 (identified in the Figures with the code CT501, CT568, CT569, CT570, CT571, CT502, CT572, CT503, CT573, CT504, CT574, CT575, CT576 and CT505, respectively).

FIGS. 12C and 12D show the bar graph and statistical data of chemotaxis migration assay results in the inhibition of HMGB1-induced NIH/3T3 cells by human HMGB1 Box-A wild type of SEQ ID NO:1 (CT500) and polypeptide variants of SEQ ID NOs:16-23 and 25-29 (identified in the Figures with the code CT577, CT578, CT506, CT579, CT580, C1581, CT507, CT582, CT584, CT508, CT509, CT510 and CT585, respectively).

FIGS. 12E and 12F show the bar graph and statistical data of chemotaxis migration assay results in the inhibition of HMGB1-induced NIH/3T3 cells by human HMGB1 Box-A wild type of SEQ ID NO:1 (CT500) and polypeptide variants of SEQ ID Nos:30-35 and 37-43 (identified in the Figures with the code CT511, CT512, CT513, CT514, CT586, CT515, CT516, CT517, CT518, CT519, CT520, CT521 and CT522, respectively).

FIGS. 12G and 12H show the bar graph and statistical data of chemotaxis migration assay results in the inhibition of HMGB1-induced NIH/3T3 cells by human HMGB1 Box-A wild type of SEQ ID NOs:44-57 (identified in the Figures with the code CT523, CT524, CT525, CT526, CT527, CT528, CT588, CT529, CT530, CT589, CT590, CT531, CT591 and CT532, respectively).

FIGS. 12I and 12J show the bar graph and statistical data of chemotaxis migration assay results in the inhibition of HMGB1-induced NIH/3T3 cells by human HMGB1 Box-A wild type of SEQ ID NO:1 (CT500) and polypeptide variants of SEQ ID Nos:58-67 and 69-71 (identified in the Figures with the code CT592, CT533, CT593, CT534, CT535, CT536, CT537, CT594, CT538, CT539, CT540, CT541 and CT542, respectively).

FIGS. 12K and 12L show the bar graph and statistical data of chemotaxis migration assay results in the inhibition of HMGB1-induced NIH/3T3 cells by human HMGB1 Box-A wild type of SEQ ID NO:1 (CT500) and polypeptide variants of SEQ ID Nos:72-85 (identified in the Figures with the code CT596, CT597, CT598, CT599, CT600, CT601, CT602, CT603, CT543, CT544, CT545, CT546, CT547 and CT604, respectively).

FIGS. 12M and 12N show the bar graph and statistical data of chemotaxis migration assay results in the inhibition of HMGB1-induced NIH/3T3 cells by human HMGB1 Box-A wild type of SEQ ID NO:1 (CT500) and polypeptide variants of SEQ ID NOs:86-99 (identified in the Figures with the code CT548, CT549, CT605, CT606, CT607, CT608, CT609, CT610, CT550, CT551, CT611, CT552, CT553 and CT554, respectively).

FIGS. 12O and 12P show the bar graph and statistical data of chemotaxis migration assay results in the inhibition of HMGB1-induced NIH/3T3 cells by human HMGB1 Box-A wild type of SEQ ID NO:1 (CT500) and polypeptide variants of SEQ ID Nos:100-113 (identified in the Figures with the code CT555, CT556, CT557, CT558, CT559, CT612, CT560, CT561, CT613, CT562, CT563, CT564, CT565 and CT566, respectively).

FIGS. 12Q and 12R show the bar graph and statistical data of chemotaxis migration assay results in the inhibition of HMGB1-induced NIH/3T3 cells by human HMGB1 Box-A wild type of SEQ ID NO:1 (CT500) and polypeptide variants of SEQ ID Nos:114-116 (identified in the Figures with the code CT567, CT614 and CT615, respectively).

FIG. 13 shows the image of the Tricine SDS-PAGE gel loaded with human HMGB1 Box-A wild type of SEQ ID NO:1 (CT500) at different timepoints after protease digestion of the protease resistance testing described in Example 7. The Box-A wild type protein tested for protease resistance is a His-tagged protein. After 5 minutes of digestion CT500 shows two major bands, one corresponding to the original protein in the sample and the second corresponding to the 84-aminoacid protein without the N-term His-tag (indicated on the figure with an arrow). The profile of this second band shows resistance to proteases for 30 minutes. Minor bands present on this and other gels of FIG. 14 to FIG. 81 correspond to Box-A digested fragments.

FIG. 14 to FIG. 81 show the image of the Tricine SDS-PAGE gel loaded with the polypeptide variants of the present invention at different timepoints after protease digestion of the protease resistance testing described in Example 7. Box-A polypeptide variants tested for protease resistance are Hig-tagged proteins. After 5 minutes of digestion the SDS-PAGE gel image of the polypeptide variants show two major bands, one corresponding to the original protein variant in the sample and the second corresponding to the Box-A 84 amino acid protein variant without the N-term His-tag.

FIG. 14 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:2 (CT501) at different timepoints after protease digestion.

FIG. 15 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:7 (CT502) at different timepoints after protease digestion.

FIG. 16 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:9 (CT503) at different timepoints after protease digestion.

FIG. 17 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:11 (CT504) at different timepoints after protease digestion.

FIG. 18 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:15 (CT505) at different timepoints after protease digestion.

FIG. 19 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:18 (CT506) at different timepoints after protease digestion.

FIG. 20: Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:22 (CT507) at different timepoints after protease digestion.

FIG. 21 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:26 (CT508) at different timepoints after protease digestion.

FIG. 22 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:27 (CT509) at different timepoints after protease digestion.

FIG. 23 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:28 (CT510) at different timepoints after protease digestion.

FIG. 24 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:30 (CT511) at different timepoints after protease digestion.

FIG. 25 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:31 (CT512) at different timepoints after protease digestion.

FIG. 26 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:32 (CT513) at different timepoints after protease digestion.

FIG. 27 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:33 (CT514) at different timepoints after protease digestion.

FIG. 28 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:35 (CT515) at different timepoints after protease digestion.

FIG. 29 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:37 (CT516) at different timepoints after protease digestion.

FIG. 30 shows the Tricine SOS-PAGE of the polypeptide variant of SEQ ID NO:38 (CT517) at different timepoints after protease digestion.

FIG. 31 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:39 (CT518) at different timepoints after protease digestion.

FIG. 32 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:40 (CT519) at different timepoints after protease digestion.

FIG. 33 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:41 (CT520) at different timepoints after protease digestion.

FIG. 34 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:42 (CT521) at different timepoints after protease digestion.

FIG. 35 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:43 (CT522) at different timepoints after protease digestion.

FIG. 36 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:44 (CT523) at different timepoints after protease digestion.

FIG. 37 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:45 (CT524) at different timepoints after protease digestion.

FIG. 38 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:46 (CT525) at different timepoints after protease digestion.

FIG. 39 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:47 (CT526) at different timepoints after protease digestion.

FIG. 40 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:48 (CT527) at different timepoints after protease digestion.

FIG. 41 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:49 (CT528) at different timepoints after protease digestion.

FIG. 42 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:51 (CT529) at different timepoints after protease digestion.

FIG. 43 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:52 (CT530) at different timepoints after protease digestion.

FIG. 44 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:55 (CT531) at different timepoints after protease digestion.

FIG. 45 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:57 (CT532) at different timepoints after protease digestion.

FIG. 46 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:59 (CT533) at different timepoints after protease digestion.

FIG. 47 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:61 (CT534) at different timepoints after protease digestion.

FIG. 48 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:62 (CT535) at different timepoints after protease digestion.

FIG. 49 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:63 (CT536) at different timepoints after protease digestion.

FIG. 50 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:64 (CT537) at different timepoints after protease digestion.

FIG. 51 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:66 (CT538) at different timepoints after protease digestion.

FIG. 52 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:67 (CT539) at different timepoints after protease digestion.

FIG. 53 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:69 (CT540) at different timepoints after protease digestion.

FIG. 54 shows the Trickle SDS-PAGE of the polypeptide variant of SEQ ID NO:70 (CT541) at different timepoints after protease digestion.

FIG. 55 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:71 (CT542) at different timepoints after protease digestion.

FIG. 56 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:80 (CT543) at different timepoints after protease digestion.

FIG. 57 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:81 (CT544) at different timepoints after protease digestion.

FIG. 58 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:82 (CT545) at different timepoints after protease digestion.

FIG. 59 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:83 (CT546) at different timepoints after protease digestion.

FIG. 60 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:84 (CT547) at different timepoints after protease digestion.

FIG. 61 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:86 (CT548) at different timepoints after protease digestion.

FIG. 62 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:87 (CT549) at different timepoints after protease digestion.

FIG. 63 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:94 (CT550) at different timepoints after protease digestion.

FIG. 64 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:95 (CT551) at different timepoints after protease digestion.

FIG. 65 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:97 (CT552) at different timepoints after protease digestion.

FIG. 66 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:98 (CT553) at different timepoints after protease digestion.

FIG. 67 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:99 (CT554) at different timepoints after protease digestion.

FIG. 68 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:100 (CT555) at different timepoints after protease digestion.

FIG. 69 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:101 (CT556) at different timepoints after protease digestion.

FIG. 70 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:102 (CT557) at different timepoints after protease digestion.

FIG. 71 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:103 (CT558) at different timepoints after protease digestion.

FIG. 72 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:104 (CT559) at different timepoints after protease digestion.

FIG. 73 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:106 (CT560) at different timepoints after protease digestion.

FIG. 74 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:107 (CT561) at different timepoints after protease digestion.

FIG. 75 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:109 (CT562) at different timepoints after protease digestion.

FIG. 76 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:110 (CT563) at different timepoints after protease digestion.

FIG. 77 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:111 (CT564) at different timepoints after protease digestion.

FIG. 78 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:112 (CT565) at different timepoints after protease digestion.

FIG. 79 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:113 (CT566) at different timepoints after protease digestion.

FIG. 80 shows the Tricine SDS-PAGE of the polypeptide variant of SEQ ID NO:114 (CT567) at different timepoints after protease digestion.

FIG. 81 shows a table in which the results of the Tricine SDS-PAGE are summarized. A cross indicates the presence on the gel of the band corresponding to the 84 amino acid long protein fragment of the HMGB1 Box-A wild-type or of the HMGB1 Box-A polypeptide variant.

EXAMPLES 1. Production of HMGB1 Box-A Native and Variants in Bacteria

The in silico generated variants of HMGB1 Box-A were cloned from HMGB1 protein into an inducible plasmid vector (FIG. 9) used to transform E. coli M15 strain competent cells. M15 cells were grown overnight in 1 mL of LB medium containing Kanamicyn and Ampicillin in 96 deep-well plates under agitation (750 rpm). At OD_(600 nm) of 0.2-0.3 the cultures were diluted in 5 mL of LB medium in 24-well plates to reach an OD_(600 nm) of 0.07.

The M15 cells were incubated at 37° C. under constant agitation (200 rpm). The production of Box-A (native or variants) was induced by the addition of IPTG (1 mM final concentration) at OD_(600 nm) of 0.6. The culture was continued for three hours at 37° C. under agitation (200 rpm). M15 cells were then harvested by centrifugation at 1000 g for 15 minutes, the supernatant was discarded and the pellet stored at −80° C. at least for 1 hour before cells lysis and Box-A purification.

2. Purification of HMGB1 box-A Native and Variants

M15 cells pellet was thawed on ice for 15 min. The cells were resuspended in 1 mL NPI-10 buffer containing 1 mg/mL Lysozyme and incubated for 30 min at RT under agitation at 750 rpm on a plate shaker. After the equilibration of Ni-NTA QIAfilter with 200 μL of Superflow resin (QIAGEN catalog#969261) and 600 μL of NPI-10 buffer the bacterial lysate was loaded and 200 μL of absolute EtOH added. Four wash steps with 1 mL of NPI-20 were performed. The second and third washes were done with 1 mL NPI-20 added with 100 μg/mL Polymyxin (Fluka catalog#81271) in order to deplete LPS contaminants. After wash steps Box-A native and variants were eluted with 450 μL NPI-250. The samples were stored at 4° C.

Box-A native and variants were re-purified with a DetoxiGel polymyxin column (PIERCE) at 4° C. according to the supplier instructions. Finally the eluted proteins were filtered (0.22 μm) in PBS and stored at 4° C. to be tested.

3. Box-A Biological Activity Assay

HMGB1 stimulates the secretion of TNF-alpha and of other cytokines as well as the proliferation of macrophages and monocytes. Box-A acts as an antagonist by inhibiting the activity of HMGB1.

The activity of Box-A native and variants produced were measured by the level of inhibition on the stimulation produced by HMGB1 on RAW 264.7 cells (murine macrophages, ATCC).

HMGB1 Box-A native and variants produced as described above were tested in a two-step process of screening directed to test i) their inhibition of HMGB1 induced TNF-alpha release and ii) their resistance to proteolysis.

In order to determine the proper HMGB1 concentration to be used in inhibition assay RAW 264.7 cells were seeded in 96 well plates (4×10⁵ cells/well) and grown overnight in RPMI 1640 medium supplemented with 0.1% BSA. After overnight culture, cells were stimulated with HMGB1 (two times serial dilution concentrations between 100 μg/mL and 0.05 μg/mL) for 24 hours. The level of TNF-alpha produced was measured from cell media using ELISA (R&D systems), according to the manufacturer instructions. As presented in FIG. 10, HMGB1 significantly stimulated TNF-alpha release in macrophage cultures.

4. Box-A Inhibition of HMGB1 TNF-Alpha Release as Screening Test

Murine macrophage-like RAW 264.7 cells were seeded in 96 well plates (4×10⁵ cells/well) and grown overnight in RPMI 1640 medium supplemented with 0.1% BSA. After overnight culture, cells were stimulated with an adequate concentration of HMGB1 and Box-A native or variants or His-tagged (two times serial dilution between 20 μg/mL and 0.5 μg/mL) for 24 hours. The level of TNF-alpha was measured from cell media using ELISA (R&D systems), according to the manufacturer instructions.

FIG. 11 shows an example of dose-dependent inhibition of HMGB1 induced TNF release by Box-A, with an EC50 of 7.5 μg/ml (solid line). 100% inhibition of TNF-alpha release is obtained with a concentration of 20 μg/ml of Box-A. In parallel, TNF-alpha levels are measured in Box-A stimulated cells without HMGB1 in order to determine the presence or absence of contaminating endotoxin in Box-A preparation and quantify any non-HMGB1 dependent release of TNF-alpha. No release of TNF-alpha is observed at all concentrations of Box-A used in the assay (dashed line).

5. Resistance to Proteolysis of Box-A Variants

Resistance of Box-A variants to proteolysis is determined as the residual biological activity (in the HMGB1/RAW cells system) following exposure to a mixture of selected proteases at increasing times of incubation.

20 μg of Box-A native or variants were treated with a mixture of proteases at 1% w/w of total proteins. The mixture of proteases was freshly prepared for each assay from stock solutions of endoproteinase Glu-C (SIGMA; 200 μg/ml), trypsin (SIGMA; 400 μg/ml) and α-chymotrypsin (SIGMA; 400 μg/ml).

Samples were collected at different time points between 5 minutes and 8 hours of incubation with proteases after stopping the reaction with the addition of 10 μl of anti-proteases solution (Roche). Biological activity of each sample was then evaluated by the screening test described above in order to assess the residual activity at each time point.

6. In Vitro Activity Testing NIH/373 Cell Migration Assay

The purpose of the present study was to evaluate the activity of each of the HMGB1 Box-A polypeptide variants of the human HMGB1 Box-A full-length fragment as defined in SEQ ID NOs:2-116 and to compare their activity to that of human wild type HMGB1 Box-A full-length fragment of SEQ ID NO:1 in order to select all the variants with similar or better activity than wild type. HMGB1 Box-A activity is evaluated in vitro as inhibition of HMGB1-induced NIH/3T3 cells migration.

6.1 Materials

-   -   HMGB1 Box-A wild type and variants (Nautilus Biotech)     -   NIH/3T3 cells (ATCC n. CRL-1658)     -   D-MEM medium (GIBCO; cat. n. 31966-021)     -   Foetal Bovine Serum (GIBCO; cat. n. 10270-106)     -   Penicillin-Streptomycin 10,000 U/ml (GIBCO; cat. n. 15140-122)     -   L-Glutamine 200 mM (GIBCO; cat. n. 25030-024)     -   TrypLE Select (GIBCO; cat. n. 12563-011)     -   Phosphate Buffered Saline (0.138 M NaCl, 0.0027 M KCl, 0.01 M         phosphate, pH 7.4)     -   PVP free filters (8 μm pore size; 13 mm total diameter) (Neuro         Probe; cat. n. PFA8)     -   Human fibronectin (Roche; cat. n. 1080938)     -   Blind Well Chemotaxis Chambers (Neuro Probe; cat. n. BW25)     -   GIEMSA Stain Modified (Sigma; cat. n. GS1L)         6.2 Filters Preparation

Polycarbonate membranes PVP free filters (8 μm pore size, 13 mm total diameter) are prepared about one hour before performing the experiment by coating them with 30 μl/filter of a solution 50 μg/ml of fibronectin dispensed on the opaque side of the filter. The stock fibronectin solution is prepared by diluting the lyophilized fibronectin in ddH₂O to a final concentration of 1 mg/ml and by keeping the solution about 1 hour at 37° C. for complete dissolution. This stock solution can be stored at −20° C.

The filters are then left to dry under the laminar flux of the hood (about one hour).

6.3 Cells Preparation

NIH/3T3 cells are seeded the day before the experiment (approximately 22-24 hours before performing the experiment) 10⁶ cells/plate.

When the filters are ready to use, the cells are detached with Trypsin, counted and resuspended 10⁶ cells/ml in serum free culture medium.

6.4 Chemotaxis Assay

In each chemotaxis experiment 14 different polypeptide variants of the human HMGB1 Box-A full-length fragment of the invention are tested.

Growth cell medium without serum addition (w/o FBS) is used as negative control representing spontaneous migration.

1 nM HMGB1 is used as positive control. HMGB1 Box-A wild type or the tested polypeptide variants 0.5/1 nM are added to 1 nM HMGB1 to inhibit HMGB1-induced NIH/3T3 cell migration.

Negative control (w/o FBS) and positive control (1 nM HMGB1) are tested in triplicate in each experiment.

HMGB1 Box-A wild type (SEQ ID NO:1) activity in inhibiting HMGB1-induced cell migration is tested in triplicate in each experiment.

Each of the HMGB1 Box-A polypeptide (SEQ ID NO:2 to 116) variants is tested in duplicate.

Blind Well Chemotaxis Chambers are used. The clean, dry lower well of each chamber is filled with 50 μl of DMEM without FBS added with the appropriate chemotactic agent and inhibitors. A slight positive meniscus should form when the well is filled; this helps prevent air bubbles from being trapped when the filter is applied. With small forceps the filter is placed over the filled well (fibronectin treated side up), being careful not to trap air bubbles and not to touch the filter with fingers. The filter retainer is screwed in by hand. Cell suspension (50000 cells/50 μl) is pipetted into the upper well and 150 μl of serum free medium are added to fill the upper well of the chamber. The filled chamber is incubated for 3 hours (37° C., 5% CO₂) to allow cell migration. After incubation the fluid is removed from the filter. The retainer is unscrewed and immersed in cool distilled water. The filter is lifted out with forceps, placed on a clean surface (solid paraffin) (migrated cells side up) and fixed with a needle (placed on the border area).

6.5 GIEMSA Staining of Migrated Cells

The filters are fixed with ethanol once and then washed three times under running water. A working solution of GIEMSA Stain Modified diluted 1:10 in ddH₂O is prepared just before use. After washing of the filters, the staining is added and left to incubate for 20 minutes. Washing of the staining is performed under running water. The filters are then placed on slides with the migrated cells side down, and the non-migrated cells side is gently wiped off with a wet cotton swab (wipe twice, using two swabs or both ends of a double-tipped swab) being careful not to move the filter. After cleaning, a cover slide is placed on the filter and cells are counted under a microscope at 40× in 10 random fields/filter.

6.6 Data Representation and Statistical Analysis

The results of the NIH/3T3 migration assay performed are reported in the tables and bar graphs shown in FIGS. 12A-12R.

Data are represented in bar columns as MEAN±95% Cl.

One-way ANOVA followed by Dunnett's post test (control column data: 1 nM HMGB1 sample+HMGB1 Box-A WT sample) is the statistical analysis performed.

When evaluating the results data, HMGB1 Box-A variants data having a post test p value <0.05 are considered significantly different from HMGB1 Box-A wild type. If the mean of the Box-A polypeptide variant is higher than that of Box-A wild type the column is coloured in red in the graph of the experiment shown in FIGS. 12A to 12R. Those red columns represent HMGB1 Box-A polypeptide variants showing less activity than wild type in inhibiting HMGB1-induced cell migration.

If the mean of the polypeptide variant results lower than that of wild type Box-A then the column is coloured in light blue in the graph of the experiment shown in FIGS. 12A to 12R. Those variants represent HMGB1 Box-A variants showing higher activity than HMGB1 Box-A wild type in inhibiting HMGB1-induced cell migration.

HMGB1 Box-A variants data having a post test p value >0.05 are considered not significantly different from HMGB1 Box-A wild type. The bar column of those variants are coloured in green. Those variants represent HMGB1 Box-A variants showing the same activity of wild type in inhibiting HMGB1-induced cell migration.

6.7 Results

The activity of polypeptide variants of the human HMGB1 high affinity binding domain Box-A of SEQ ID NOs:2 to 116 was evaluated in comparison to human HMGB1 Box-A wild-type of SEQ ID NO:1 as inhibition of HMGB1-induced cell migration.

The chemotaxis assays results revealed (FIGS. 12A to 12R) that for 26 polypeptide variants the mutation according to the present invention could lead to a higher activity in cell migration inhibition in comparison with the activity of the wild-type human HMGB1 Box-A. In particular, a higher activity in cell migration inhibition was shown for the polypeptide variants of SEQ ID NOs: 30-32, 35, 38, 40-41, 43, 48, 51, 57, 63-64, 69, 70, 94, 95, 100, 103-104, 106-107, 109-111 and 113.

Moreover, the chemotaxis assays results revealed (FIGS. 12A to 12R) that 41 polypeptide variants showed no changes in their activity in inhibiting HMGB1-induced cell migration compared to the activity of Box-A wild-type polypeptide. In particular, this is the case for the polypeptide variants of SEQ ID NOs: 2, 7, 9, 11, 15, 18, 22, 26-28, 33, 37, 39, 42, 44-47, 49, 52, 55, 59, 61, 62, 66-67, 71, 80-84, 86-87, 97-99, 101-102, 112 and 114.

All these Box-A polypeptide variants which exhibit a similar or a higher activity than the Box-A wild-type were tested for in vitro protease resistance, in order to choose the most resistant ones that are at least as active as Box-A wild-type (see protease resistance test in Example 7).

7. In Vitro Protease Resistance Testing

The purpose of the present study was to evaluate the in vitro protease resistance of to HMGB1 Box-A variants shown in Example 6 and to compare it to that of wild type HMGB1 Box-A of SEQ ID NO:1 in order to identify the variants with improved protease resistance with respect to wild type polypeptide.

7.1 Materials

-   -   HMGB1 His-tagged Box-A wild type and selected variants (Nautilus         biotech)     -   Trypsine (Sigma; cat. n. T8658; lot.n. 045K5113)     -   α-chymotrypsine (Sigma; cat. n. C6423; lot.n. 109H74858),     -   Endoproteinase Asp-N (Sigma; cat. n. P3303; lot.n. 046K1049)     -   Endoproteinase Glu-C(Sigma; cat. n. P6181; lot.n. 075K5100)     -   Complete, Mini EDTA-free protease inhibitor cocktail (Roche;         cat. n. 11836170 001)     -   Trizma base (Sigma; cat. n. T6066)     -   Acrilamide/bis solution 40% in water (Sigma; cat.n. 01709)     -   SDS (Sigma; cat. n. 71729)     -   Glycerol 99% (Sigma; cat. n. G9012)     -   Temed (Sigma; cat. n. 87689)     -   APS (Sigma; cat. n. A 3678)     -   Polypeptide SDS-PAGE Molecular Weight Standards (Bio-Rad;         cat. n. 161-0326)     -   Premixed 10× Tris/tricine/SDS Buffer (Bio-Rad; cat. n. 161-0744)     -   β-Mercaptoethanol (Sigma; cat. n. M7154)     -   Methanol (VWR; cat. n. 20864.320)     -   Acetic acid (VWR; cat. n. 20104.323)     -   Brilliant Blue R (Sigma; cat. n. 80149)     -   Bromophenol Blue (Sigma; cat. n. B0126)     -   Hydrochloric acid (Merck; cat. n. 1.00319.2511)     -   3× sample loading buffer for Tricine gels (composition: 150 mM         Tris-HCl, pH 6.8; 12% SDS; 36% glycerol; 6% 3-Mercaptoethanol;         0.04% of bromophenol blue)         7.2. Protease Mixture Preparation

A mixture of proteases containing trypsine, α-chymotrypsine, endoproteinase Asp-N and endoproteinase Glu-C is used.

Table 1 reports specificity of each of the proteases used in this study.

TABLE 1 protease specificity. Protease Specificity Tripsin C-term of K, R (not if P at C-term of cutting site; slower digestion if acidic residue on either side of cutting site) α-chymotrypsin C-term of T, P, W, L (secondary hydrolysis: C-term of M, I, S, T, V, H, G, A) Endoproteinase Asp-N N-term of D, C Endoproteinase Glu C-term of E, D (not if P is at C-term of cutting site)

Each lyophilized protease is dissolved according to Manufacturer recommendations to obtain a stock solution that is aliquoted and stored at −80° C.

100 μg of trypsin are dissolved in 100 μl of dH₂O to obtain a 1 μg/μl stock solution. 25 μg of α-chymotrypsine are dissolved in 50 μl of a solution 1 mM HCl, 2 mM CaCl₂ to obtain a 0.5 μg/μl stock solution. 2 μg of endoproteinase Asp-N are dissolved in 50 μl of dH₂O to obtain a 0.04 μg/μl stock solution. 25 μg of endoproteinase Glu-C are dissolved in 50 μl of dH₂O to obtain a 0.5 μg/μl stock solution.

Before performing the experiment one aliquot of each protease stock solution is left to thaw on ice.

Trypsin and endoproteinase Glu-C stock aliquots are diluted in dH₂O to obtain a final working solution of 0.1 μg/μl. α-chymotrypsine stock aliquot is diluted in a solution 1 mM HCl, 2 mM CaCl₂ to obtain a final 0.1 μg/μl working solution. Endoproteinase Asp-N aliquot is used without dilution.

Just before performing the experiment a mixture of proteases containing 1% (in weight/weight of total Box-A contained in the sample) of each protease is freshly prepared and immediately added to HMGB1 Box-A to be digested.

7.3. HMGB1 Box-A Wild Type and Variants Protease Digestion

18 μg total of each HMGB1 Box-A (wild type or variants) are digested in each experiment.

HMGB1 Box-A to be tested is left to thaw on ice and the volume corresponding to 18 μg is taken. The volume of this solution is then brought with dH₂O to a final volume of 90 μl in order to obtain the same final volume for each HMGB1 Box-A to be tested.

10 μl of this solution (corresponding to 2 μg of HMGB1 Box-A) are taken before adding the protease mixture. This sample corresponds to “time 0” not digested sample.

The remaining sample (16 μg of HMGB1 Box-A) is added with 8.8 μl (corresponding to 0.16 μg of each protease of the freshly prepared mixture; see 7.2) of protease mixture for digestion.

Protease digestion is performed at 25° C. and a volume corresponding to 2 μg of HMGB1 Box-A (originally present in the mixture) is sampled at defined time points. Digestion is stopped adding 4 μl of a solution of complete Mini EDTA-free protease inhibitor cocktail (1 tablet dissolved in 10 ml of dH₂O).

Timepoints for sampling are: 0, 5 minutes, 15 minutes, 30 minutes, 1 hour, 1.5 hours, 2 hours and 4 hours.

Soon after protease inhibition, samples are added with the appropriate amount of sample loading buffer 3× and incubated at 95° C. for about 3 minutes.

7.4. Tricine SDS-PAGE of Digested HMGB1 Box-A Wild Type and Variants

After protease digestion and samples preparation, timepoints samples of each HMGB1 Box-A are loaded on a Tricine SDS PAGE gel (see for references: Schägger and von Jagow, “Tricine-sodium dodecyl sulphate-polyacrylamide gel electrophoresis for the separation of proteins in the range from 1 to 100 kDa”, Anal. Biochem. 166, 368-379, 1987).

5 μl of Polypeptide SDS-PAGE Molecular Weight Standards (Bio-Rad) are loaded for reference on each gel.

Each well of the gel is loaded with 10 μl of sample (volume corresponding to 1 μg of HMGB1 Box-A before digestion).

Electrophoresis is performed at 30 V until the bromophenol blue has entered the separating portion of the gel, then at 120 V (Mini Protean 3 System; Bio-Rad) till the end of the run.

Gels are stained by soaking in a Coomassie Brilliant Blue R staining solution (0.1% w/v in 50% methanol, 10% acetic acid) for 1 hour and destained overnight in destaining solution (30% methanol, 10% acetic acid).

Gel images are acquired with Gel Doc 2000 (Bio-Rad) imaging system.

7.5 Results

In the above reported assay conditions HGMB1 wild-type protein resisted approximately 30 minutes to complete protease digestion. In FIG. 13 the band corresponding to the 84-amino acid full-length fragment of human HMGB1 Box-A wild-type of SEQ ID NO:1 protein is visible until 30 minutes of protease digestion.

21 Box-A polypeptide variants tested showed an increased resistance to protease (FIG. 15). In the reported assay conditions these variants resist from 1 hour to 2 hours to protease digestion. The polypeptide variants of SEQ ID NOs: 33, 35, 37, 38, 39, 42, 43, 44, 47, 48, 57, 62, 69 and 104 showed a resistance of 1 hour to protease digestion. FIGS. 27-31, 34-36, 39-40, 45, 48, 53 and 72 show a band corresponding to the not His-tagged protein of 84 amino acids which is visible until 1 hour of protease digestion.

The polypeptide variants of SEQ ID NOs: 45, 49, 52, 55 and 67 showed a resistance of 1.5 hours to protease digestion. FIGS. 37, 41, 43, 44 and 52 show a band corresponding to the not His-tagged protein of 84 amino acids which is clearly visible 1 hour and a half after protease digestion. The polypeptide variants of SEQ ID NOs: 59 and 64 even show a resistance of up to 2 hours to protease digestion. FIGS. 46 and 50 show a band of the not His-tagged protein of 84 amino acids which is clearly visible until 2 hours after protease digestion.

REFERENCES

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1. An isolated polypeptide variant of HMGB1 high affinity binding domain Box-A (HMGB1 Box-A) having an amino acid sequence selected from the group consisting of SEQ ID NOs.: 33, 35, 37-39, 42-45, 47-49, 52, 55, 57, 62, 67, 69, and
 104. 2. A medicament comprising the polypeptide variant of claim 1 as an active agent.
 3. A pharmaceutical composition comprising an effective amount of at least one polypeptide variant of claim 1 as an active agent and a pharmaceutically acceptable carrier.
 4. The composition of claim 3 wherein the at least one polypeptide variant is in combination with at least one further agent.
 5. The composition of claim 3, further comprising ingredients suitable for therapeutic applications. 